MolNFT v1 · #66347 · protein
Crystal structure of pyrophosphate-dependent phosphofructokinase from nitrosospira multiformis. northeast structural genomics consortium target id NMR42
3HNO: “Crystal structure of pyrophosphate-dependent phosphofructokinase from nitrosospira multiformis. northeast…”. X-ray diffraction, 1 ligand (BR), 14 pockets (best druggability 0.73). MolNFT v1 #66347 on GenesisL1: 3D structure, binding…
- PDB
- 3HNO
- Type
- protein
- Length
- 1,579 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrophosphate-dependent phosphofructokinase
- EC
- 2.7.1.90
- UniProt
- Q2YB24
- Ligands
- BR
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Pyrophosphate-dependent phosphofructokinase (EC 2.7.1.90) | protein | 395 | 42% helix, 19% strand | Q2YB24 |
| D | Pyrophosphate-dependent phosphofructokinase (EC 2.7.1.90) | protein | 394 | 41% helix, 19% strand | Q2YB24 |
Ligands and binding sites
- BR · Bromide ion · ion · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.73 | 0.77 | 92 | empty |
| 2 | 440 | 0.72 | 0.83 | 48 | empty |
| 3 | 298 | 0.56 | 0.77 | 48 | empty |
| 4 | 249 | 0.55 | 0.77 | 46 | empty |
| 5 | 231 | 0.53 | 0.77 | 37 | empty |
Interfaces
4 interfaces between chains.
- C–D · 625 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 283 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 114 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 80 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3HNO · Crystal Structure of Pyrophosphate-dependent phosphofructokinase from Nitrosospira… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q2YB24
- Elsewhere: RCSB PDB 3HNO · PDBe 3HNO · UniProt Q2YB24
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